@inproceedings{LafondBSStrikesAgainstPhageRecombination,
author = {M. Lafond and
A. Bergeron and
K.M. Swenson},
title = {Two Strikes Against the Phage Recombination Problem},
booktitle = {Proc.\ 20th Workshop\ Comp.\ Genomics ({RECOMB-CG'23})},
pages = {68--83},
series = {Lecture Notes in Computer Science},
year = {2023},
volume = {13883},
doi = {10.1007/978-3-031-36911-7_5},
commentpdf = {../papers/2023-LafondBSStrikesAgainstPhageRecombination.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2023-LafondBSStrikesAgainstPhageRecombination.pdf}{PDF}}
}
@inproceedings{SwensonEVMW2022,
author = {K.M. Swenson and
A. Elghraoui and
F. Valafar and
S. Mirarab and
M. Weller},
title = {Quantifying Hierarchical Conflicts in Homology Statements},
booktitle = {Proc.\ 19th Workshop\ Comp.\ Genomics ({RECOMB-CG'22})},
pages = {146--167},
series = {Lecture Notes in Computer Science},
year = {2022},
volume = {13234},
doi = {10.1007/978-3-031-06220-9_9},
commentpdf = {../papers/2022-SwensonEVMWHierarchicalHomology.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2022-SwensonEVMWHierarchicalHomology.pdf}{PDF}}
}
@inproceedings{BergeronMVS2022,
author = {A. Bergeron and
M-J. Meurs and
R. Valiquette-Labont\'e and
K.M. Swenson},
title = {On the Comparison of Bacteriophage Populations},
booktitle = {Proc.\ 19th Workshop\ Comp.\ Genomics ({RECOMB-CG'22})},
pages = {3--20},
series = {Lecture Notes in Computer Science},
year = {2022},
volume = {13234},
doi = {10.1007/978-3-031-06220-9_1},
commentpdf = {../papers/2022-BergeronMLSComparisonBacteriophages.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2022-BergeronMLSComparisonBacteriophages.pdf}{PDF}}
}
@inproceedings{SimonaitisCS2019,
author = {P. Simonaitis and
A. Chateau and
K.M. Swenson},
title = {Weighted Minimum-Length Rearrangement Scenarios},
booktitle = {Proc.\ 19th Int'l Workshop Algs.\ in Bioinformatics ({WABI'19})},
pages = {13:1--13:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
isbn = {978-3-95977-123-8},
issn = {1868-8969},
year = {2019},
volume = {143},
address = {Dagstuhl, Germany},
doi = {10.4230/LIPIcs.WABI.2019.13},
commentpdf = {../papers/2019-SimonaitisWeightedRearrangement.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-SimonaitisWeightedRearrangement.pdf}{PDF}}
}
@inproceedings{TruszkowskiGS2019,
author = {J. Truszkowski and O. Gascuel and K.M. Swenson},
title = {Rapidly Computing the Phylogenetic Transfer Index},
booktitle = {Proc.\ 19th Int'l Workshop Algs.\ in Bioinformatics ({WABI'19})},
pages = {20:1--20:12},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
isbn = {978-3-95977-123-8},
issn = {1868-8969},
year = {2019},
volume = {143},
address = {Dagstuhl, Germany},
doi = {10.4230/LIPIcs.WABI.2019.20},
commentpdf = {../papers/2019-TruszkowskiRapidTransferIndex.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2019-TruszkowskiRapidTransferIndex.pdf}{PDF}}
}
@inproceedings{SimonaitisCS2018,
author = {P. Simonaitis and
A. Chateau and
K.M. Swenson},
title = {A General Framework for Genome Rearrangement with Biological Constraints},
booktitle = {Proc.\ 16th Workshop\ Comp.\ Genomics ({RECOMB-CG'18})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Bioinformatics},
volume = 11183,
year = 2018,
pages = {49-71},
doi = {10.1007/978-3-030-00834-5_3},
commentpdf = {../papers/2018-SimonaitisFrameworkRearrangement.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2018-SimonaitisFrameworkRearrangement.pdf}{PDF}~$^*$}
}
@inproceedings{PulicaniSRS2017,
author = {S. Pulicani and
P. Simonaitis and
E. Rivals and
K.M. Swenson},
title = {Rearrangement Scenarios Guided by Chromatin Structure},
booktitle = {Proc.\ 15th Workshop\ Comp.\ Genomics ({RECOMB-CG'17})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Bioinformatics},
volume = 10562,
year = 2017,
pages = {141-155},
doi = {10.1007/978-3-319-67979-2_8},
commentpdf = {../papers/2017-PulicaniGuidedRearrangements.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2017-PulicaniGuidedRearrangements.pdf}{PDF}}
}
@inproceedings{SimonaitisS2017,
author = {P. Simonaitis and K.M. Swenson},
title = {{Finding Local Genome Rearrangements}},
booktitle = {Proc.\ 17th Int'l Workshop Algs.\ in Bioinformatics ({WABI'17})},
pages = {24:1--24:13},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
isbn = {978-3-95977-050-7},
issn = {1868-8969},
year = {2017},
volume = {88},
address = {Dagstuhl, Germany},
doi = {10.4230/LIPIcs.WABI.2017.24},
commentpdf = {../papers/2017-SimonaitisFindingLocalWABI.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2017-SimonaitisFindingLocalWABI.pdf}{PDF}~$^*$}
}
@inproceedings{SwensonB2015,
title = {Models and Algorithms for Genome Rearrangement with Positional Constraints},
author = {K.M. Swenson and M. Blanchette},
booktitle = {Proc.\ 15th Int'l Workshop Algs.\ in Bioinformatics ({WABI'15})},
pages = {243-256},
year = 2015,
publisher = {Springer Verlag, Berlin},
doi = {http://dx.doi.org/10.1007/978-3-662-48221-6_18},
commentpdf = {../papers/2015-SwensonPositionalRearrangements.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2015-SwensonPositionalRearrangements.pdf}{PDF}~$^*$}
}
@inproceedings{LafondSE12,
author = {M. Lafond and
K.M. Swenson and
N. El-Mabrouk},
title = {An optimal reconciliation algorithm for gene trees with polytomies},
booktitle = {Proc.\ 12th Int'l Workshop Algs.\ in Bioinformatics ({WABI'12})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 7534,
year = 2012,
pages = {106-122},
doi = {http://dx.doi.org/10.1007/978-3-642-33122-0_9},
commentpdf = {../papers/2012-LafondOptimalReconciliationPolytomies.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-LafondOptimalReconciliationPolytomies.pdf}{PDF}}
}
@inproceedings{HollowaySAM12,
author = {P. Holloway and
K.M. Swenson and
D. Ardell and
N. El-Mabrouk},
title = {Evolution of genome organization by duplication and loss: an alignment approach},
booktitle = {Proc.\ 16th Ann.\ Int'l Conf.\ Comput.\ Mol.\ Biol.\ ({RECOMB'12})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 7262,
year = 2012,
isbn = {978-3-642-29626-0},
doi = {http://dx.doi.org/10.1007/978-3-642-29627-7_10},
pages = {94-112},
commentpdf = {../papers/2012-HollowayDupLossAlignment.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-HollowayDupLossAlignment.pdf}{PDF}~$^*$}
}
@inproceedings{OuangraouaSB12,
author = {A. Ouangraoua and
K.M. Swenson and
A. Bergeron},
title = {On the comparison of sets of alternative transcripts},
booktitle = {Proc.\ 8th Inter. Symp. on Bioinform. and Applic. ({ISBRA'12})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 7292,
year = 2012,
pages = {201-212},
doi = {http://dx.doi.org/10.1007/978-3-642-30191-9_19},
commentpdf = {../papers/2012-OuangraouaSetsOfTranscripts.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2012-OuangraouaSetsOfTranscripts.pdf}{PDF}}
}
@inproceedings{SwensonCPS11,
author = {K.M. Swenson and
E. Chen and
N.D. Pattengale and
D. Sankoff},
title = {The kernel of maximum agreement subtrees},
booktitle = {Proc.\ 7th Inter. Symp. on Bioinform. and Applic. ({ISBRA'11})},
publisher = {Springer Verlag, Berlin},
volume = 6674,
series = {Lecture Notes in Computer Science},
year = 2011,
pages = {123-135},
doi = {http://dx.doi.org/10.1007/978-3-642-21260-4_15},
commentpdf = {../papers/2011-SwensonKAST.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-SwensonKAST.pdf}{PDF}~$^*$}
}
@inproceedings{ZhengSLS11,
author = {C. Zheng and
K.M. Swenson and
E. Lyons and
D. Sankoff},
title = {{OMG}! orthologs in multiple genomes - competing graph-theoretical formulations},
booktitle = {Proc.\ 11th Int'l Workshop Algs.\ in Bioinformatics ({WABI'11})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 6833,
year = 2011,
pages = {364-375},
doi = {http://dx.doi.org/10.1007/978-3-642-23038-7_30},
commentpdf = {../papers/2011-ZhengOMG.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2011-ZhengOMG.pdf}{PDF}}
}
@inproceedings{SwensonBS10,
author = {K.M. Swenson and
G. Badr and
D. Sankoff},
title = {Listing all sorting reversals in quadratic time},
booktitle = {Proc.\ 10th Int'l Workshop Algs.\ in Bioinformatics ({WABI'10})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 6293,
year = 2010,
pages = {102-110},
doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9},
commentpdf = {../papers/2010-SwensonAllSortingRevs.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-SwensonAllSortingRevs.pdf}{PDF}~$^*$}
}
@inproceedings{OuangraouaBS10,
author = {A. Ouangraoua and
A. Bergeron and
K.M. Swenson},
title = {Ultra-perfect sorting scenarios},
booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'10})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 6398,
year = 2010,
pages = {50-61},
doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9},
commentpdf = {../papers/2010-OuangraouaUltraPerfect.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-OuangraouaUltraPerfect.pdf}{PDF}~$^*$}
}
@inproceedings{OuangraouaSC10,
author = {A. Ouangraoua and
K.M. Swenson and
C. Chauve},
title = {An approximation algorithm for computing a parsimonious first speciation in the gene duplication model},
booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'10})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 6398,
year = 2010,
pages = {290-302},
doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9},
commentpdf = {../papers/2010-OuangraouaParsimoniousFirstSpec.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-OuangraouaParsimoniousFirstSpec.pdf}{PDF}~$^*$}
}
@inproceedings{PattengaleSM10,
author = {N.D. Pattengale and
K.M. Swenson and
B.M.E. Moret},
title = {Uncovering Hidden Phylogenetic Consensus},
booktitle = {Proc. Bioinformatics Research and Applications, 6th International
Symposium, ISBRA'10},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 6053,
year = 2010,
pages = {128-139},
doi = {http://dx.doi.org/10.1007/978-3-642-13078-6_16},
commentpdf = {../papers/2010-PattengaleUncoveringConsensus.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-PattengaleUncoveringConsensus.pdf}{PDF}~$^*$}
}
@inproceedings{BadrSS10,
author = {G. Badr and
K.M. Swenson and
D. Sankoff},
title = {Listing all parsimonious reversal sequences: new algorithms and perspectives},
booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'10})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 6398,
year = 2010,
pages = {39-48},
doi = {http://dx.doi.org/10.1007/978-3-642-15294-8_9},
commentpdf = {../papers/2010-BadrAllParsimoniousSequences.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2010-BadrAllParsimoniousSequences.pdf}{PDF}~$^*$}
}
@inproceedings{SwensonRLM09,
author = {K.M. Swenson and
V. Rajan and
Y. Lin and
B. M. E. Moret},
title = {Sorting signed permutations by inversions in ${O}(n \log n)$ time},
booktitle = {Proc.\ 13th Ann.\ Int'l Conf.\ Comput.\ Mol.\ Biol.\ ({RECOMB'09})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 5541,
year = 2009,
pages = {386-399},
doi = {http://dx.doi.org/10.1007/978-3-642-02008-7_28},
commentpdf = {../papers/2009-SwensonSortingFastOLD.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2009-SwensonSortingFastOLD.pdf}{PDF}~$^*$}
}
@inproceedings{Swe08,
author = {K.M. Swenson and W. Arndt and J. Tang and B.M.E. Moret},
title = {Phylogenetic reconstruction from complete gene orders of whole genomes},
booktitle = {Proc.\ 6rd Asia Pacific Bioinformatics Conf.\ ({APBC'08})},
pages = {241-250},
year = 2008,
commentpdf = {../papers/2008-SwensonPhyloCompleteGeneOrders.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2008-SwensonPhyloCompleteGeneOrders.pdf}{PDF}}
}
@inproceedings{SwensonLRM08,
author = {K.M. Swenson and
Y. Lin and
V. Rajan and
B.M.E. Moret},
title = {Hurdles Hardly Have to Be Heeded},
booktitle = {Proc.\ 6th Workshop\ Comp.\ Genomics ({RECOMB-CG'08})},
publisher = {Springer Verlag, Berlin},
series = {Lecture Notes in Computer Science},
volume = 5267,
year = 2008,
pages = {241-251},
doi = {http://dx.doi.org/10.1007/978-3-540-87989-3_18},
commentpdf = {../papers/2008-SwensonHHHH.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2008-SwensonHHHH.pdf}{PDF}~$^*$}
}
@inproceedings{SwensonF,
author = {K.M. Swenson and N.D. Pattengale and B.M.E. Moret},
title = {A framework for orthology assignment from gene rearrangement data},
booktitle = {Proc.\ 3nd Workshop\ Comp.\ Genomics ({RECOMB-CG'05})},
publisher = {Springer Verlag, Berlin},
pages = {153-166},
year = 2005,
doi = {http://dx.doi.org/10.1007/11554714_14},
commentpdf = {../papers/2005-SwensonFrameworkOrthologyAssignment.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2005-SwensonFrameworkOrthologyAssignment.pdf}{PDF}}
}
@inproceedings{swenson2005,
author = {K.M. Swenson and M. Marron and J.V. Earnest-DeYoung and B.M.E. Moret},
title = {Approximating the true evolutionary distance between two genomes},
year = 2005,
booktitle = {Proc.\ 7th SIAM Workshop on Algorithm Engineering \& Experiments ({ALENEX'05})},
publisher = {{SIAM Press, Philadelphia}},
pages = {121-129},
doi = {http://www.siam.org/meetings/alenex05/papers/11submission.pdf},
commentpdf = {../papers/2005-SwensonApproxTrueEvolDist.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2005-SwensonApproxTrueEvolDist.pdf}{PDF}~$^*$}
}
@inproceedings{Marron-cocoon,
author = {M. Marron and K.M. Swenson and B.M.E. Moret},
year = 2003,
title = {Genomic distances under deletions and insertions},
booktitle = {Proc.\ 9th Int'l\ Conf.\ Computing and Combinatorics ({COCOON'03})},
pages = {537-547},
series = {Lecture Notes in Computer Science},
volume = 2697,
publisher = {Springer Verlag, Berlin},
doi = {http://dx.doi.org/10.1007/3-540-45071-8_54},
commentpdf = {../papers/2004-MarronDistInsDel.pdf},
note = {\href{http://www2.lirmm.fr/~swenson/papers/2004-MarronDistInsDel.pdf}{PDF}~$^*$}
}
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